This document is a presentation on using Linux for bioinformatics, covering essential commands and techniques such as bash command chaining, aliases, and file searching with 'locate' and 'find'. It explains how to utilize a .bashrc file for aliases and customization, as well as command substitution for managing data. The document also provides practical examples and a few exercises to reinforce learning.

1. This presentation is available under the Creative Commons
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hereof.
Introduction to Linux
for Bioinformatics
Productivity
Joachim Jacob
5 and 12 May 2014

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Multiple commands
In bash, commands put on one line when be
separated by “;”
$ wget http://homepage.tudelft.nl/19j49/t-
SNE_files/tSNE_linux.tar.gz ; tar xvfz tSNE_linux.tar.gz

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Multiple commands
Commands on a oneliner can also be separated by
&& or ||.
&& Only execute the command if the preceding one
finished correctly.
$ curl corz.org/ip && echo 'n'
|| (not a pipe!) - Inverse of the above. Only execute
the command if the preceding one did not succesfully
ends.

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Piping a list of files with xargs
A pipe reads the output of a command.
Some commands requires the file name to be
passed, instead of the content of the file. E.g. this
doesn't work:
$ ls | less
$ ls | file
Usage: file [-bchikLlNnprsvz0] [--apple] [--mime-
encoding] [--mime-type]
[-e testname] [-F separator] [-f
namefile] [-m magicfiles] file ...
file -C [-m magicfiles]
file [--help]

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Piping a list of files with xargs
Some commands requires the file name to be
passed, instead of the content of the file.
xargs passes the output of a command as a list of
arguments to another program.
$ ls | xargs file
bin: directory
buddy.sh: Bourne-Again shell
script, ASCII text executable
Compression_exercise: directory
Desktop: directory
Documents: directory
Downloads: directory
FastQValidator.0.1.1.tgz: gzip compressed data,
from Unix, last modified: Fri Oct 19 16:44:23 2012

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.bashrc
~/.bashrc is a hidden configuration file for bash in
your home.
It configures the prompt in your terminal.
It contains aliases to commands.

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alias example
When you enter a first word on the command line that
bash does not recognize as a command, it will
search in the aliases for the word.
You can specify aliases in .bashrc. An example:

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Alias example
Some interesting aliases
alias ll='ls -lh'
alias dirsize="du -sh */"
alias uncom='grep -v -E "^#|^$"'
alias hosts="cat /etc/hosts"
alias dedup="awk '! x[$0]++' "
Aliases are perfectly suited for storing one-liners: find
some at
https://wikis.utexas.edu/display/bioiteam/Scott%27s+li
st+of+linux+one-liners

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Alias exercise
→ exercise link

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Finding stuff: locate
Extremely quick and convenient:
locate
However, it won't find the newest files you created.
First you need to update the database by running:
updatedb
It accepts wildcards. Example:
$ locate *.sam
Bonus: How to filter on a certain location?

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Finding stuff: find
More elaborate tool to find stuff:
$ find -name alignment.sam
Find won't find without specifying options:
-name : to search on the name of the file
-type : to search for the type: (f)ile, (d)irectory, (l)ink
-perm : to search for the permissions (111 or rwx)
…
This is the power tool to find stuff.

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Finding stuff: find
The most powerful option of find:
-exec Execute a command on the found entities.

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Finding stuff: find
The most powerful option of find:
-exec Execute a command on the found entities.
$ find -name *.gz
./DRR000542_2.fastq.subset.gz
./DRR000542_1.fastq.subset.gz
./DRR000545_2.fastq.subset.gz
./DRR000545_1.fastq.subset.gz
$ find -name *.gz -exec gunzip {} ;
$ ls
DRR000542_1.fastq.subset DRR000545_1.fastq.subset
DRR000542_2.fastq.subset DRR000545_2.fastq.subset

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Command substitution in bash
In bash, the output of commands can be directly
stored in a variable. Put the command between back-
ticks.
$ test=`ls -l`
$ echo $test
total 7929624 -rw-rw-r-- 1 joachim joachim 15326 May 10
2013 0538c2b.jpg -rw-rw-r-- 1 joachim joachim 4914797 Nov
8 16:15 18d7alY

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Command substitution in bash
A variable can also contain a list. A list contains
several entities (e.g. files).
Extracting first 100k lines from compressed text file:
for filename in `ls DRR00054*tar.gz`;
do zcat $filename | head -n 1000000
>${file%.gz}.subset; done
The output of ls is being put in a list. 'for' assigns one after the other
the name of the file to the variable file. This variable is used in the
oneliner zcat | head.

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Keywords
.bashrc
;
alias
prompt
locate
find
Command substitution
Write in your own words what the terms mean

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Exercises
→ Concatenate the contents of fastq files